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planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/krocus commit 5d1d3bd35e5cf4bcffe3e7ad1b079eeff1162ca0-dirty
author thanhlv
date Fri, 15 Nov 2019 13:47:02 +0000
parents d3ccbecf8f7f
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d3ccbecf8f7f planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/krocus commit 15e535fd467e72874790ae7efd039237709b11ba-dirty
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1 <tool id="krocus" name="krocus" version="@VERSION@">
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2 <description>Multi-locus sequence typing (MLST) from uncorrected long reads</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="version_command" />
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8 <command detect_errors="exit_code"><![CDATA[
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9 krocus
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10 --output_file detected_mlst.tsv
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11 #if $opt_args.filtered_reads
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12 --filtered_reads_file filtered_reads.fq
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13 #end if
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14 --max_gap $opt_args.max_gap
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15 --min_kmers_for_onex_pass $opt_args.min_kmers_for_onex_pass
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16 --margin $opt_args.margin
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17 --min_block_size $opt_args.min_block_size
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18 --min_fasta_hits $opt_args.min_fasta_hits
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19 --min_kmers_for_onex_pass $opt_args.min_kmers_for_onex_pass
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20 --max_kmers $opt_args.max_kmers
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21 --print_interval $opt_args.print_interval
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22 --kmer $opt_args.kmer
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23 $opt_args.divisible_by_3
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24 $opt_args.verbose
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25 '$krocus_mlst_databases.fields.path' '$fastq'
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26 ]]>
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27 </command>
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28 <inputs>
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29 <param name="fastq" type="data" format="fastqsanger,fastqsanger.gz" label="Select fastq dataset" help="Specify dataset with single read"/>
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30 <param label="Select a database" name="krocus_mlst_databases" type="select">
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31 <options from_data_table="krocus_mlst_databases">
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32 <validator message="No database is available" type="no_options" />
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33 </options>
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34 </param>
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35 <section name="opt_args" title="Optional Arguments">
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36 <param name="filtered_reads" type="boolean" truevalue="" falsevalue="" checked="false" label="Save filtered reads ?"/>
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37 <param argument="--max_gap" type="integer" min="1" value="4" label="Maximum gap for blocks to be contigous, measured in
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38 multiples of the k-mer size" help="Default:4" />
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39 <param argument="--margin" type="integer" min="1" value="10" label="Flanking region around a block to use for mapping" help="Default:10" />
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40 <param argument="--min_block_size" type="integer" min="1" value="150" label="Minimum block size in bases" help="Default:150" />
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41 <param argument="--min_fasta_hits" type="integer" min="1" value="10" label="Minimum No. of kmers matching a read" help="Default:10" />
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42 <param argument="--min_kmers_for_onex_pass" type="integer" min="2" value="5" label="Minimum No. of kmers matching a read in 1st pass" help="Default:5" />
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43 <param argument="--max_kmers" type="integer" min="1" value="10" label="Dont count kmers occuring more than this many times" help="Default:10" />
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44 <param argument="--print_interval" type="integer" min="1" value="10" label="Print ST every this number of reads" help="(Default:500)" />
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45 <param argument="--kmer" type="integer" min="2" value="10" label="k-mer size" help="(Default:11)" />
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46 <param argument="--divisible_by_3" type="boolean" truevalue="--divisible_by_3" falsevalue="" checked="false" label="Genes which are not divisible by 3 are excluded" help="(Default:No)" />
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47 <param argument="--verbose" type="boolean" truevalue="--verbose" falsevalue="" checked="false" label="Turn on debugging" help="(Default:No)" />
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48 </section>
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49 </inputs>
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50
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51 <outputs>
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52 <data name="output_file" format="tabular" label="${tool.name} on ${on_string}: Output" from_work_dir="detected_mlst.tsv"/>
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53 <data name="filtered_reads" format="fastq" label="${tool.name} on ${on_string}: Filtered reads" from_work_dir="filtered_reads.fq">
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54 <filter>opt_args['filtered_reads'] is True</filter>
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55 </data>
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56 </outputs>
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57
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58 <tests>
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59 <test expect_num_outputs="1">
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60 <param name="fastq" value="pacbio.fastq.gz" ftype="fastqsanger" />
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61 <param name="krocus_mlst_databases" value="mlst_db"/>
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62 <output name="output_file" ftype="tabular" file="mlst_output_pacbio.tsv" compare="sim_size" />
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63 </test>
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64 <test expect_num_outputs="2">
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65 <param name="fastq" value="pacbio.fastq.gz" ftype="fastqsanger" />
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66 <param name="filtered_reads" value="True" />
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67 <param name="krocus_mlst_databases" value="mlst_db"/>
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68 <output name="filtered_reads" ftype="fastq" file="filtered_reads.fq" compare="sim_size" />
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69 </test>
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70 </tests>
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72 <help><![CDATA[
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73 Multi-locus sequence typing (MLST) from uncorrected long reads
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74
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75 Krocus can predict a sequence type directly from uncorrected long reads, and
3e434415a387 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/krocus commit 5d1d3bd35e5cf4bcffe3e7ad1b079eeff1162ca0-dirty
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76 which was designed to consume read data as it is produced, providing results
3e434415a387 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/krocus commit 5d1d3bd35e5cf4bcffe3e7ad1b079eeff1162ca0-dirty
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77 in minutes. It is the only tool which can do this from uncorrected long
3e434415a387 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/krocus commit 5d1d3bd35e5cf4bcffe3e7ad1b079eeff1162ca0-dirty
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78 reads. We tested Krocus on over 600 samples sequenced with using long read
3e434415a387 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/krocus commit 5d1d3bd35e5cf4bcffe3e7ad1b079eeff1162ca0-dirty
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79 sequencing technologies from PacBio and Oxford Nanopore. It provides
3e434415a387 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/krocus commit 5d1d3bd35e5cf4bcffe3e7ad1b079eeff1162ca0-dirty
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80 sequence types on average within 90 seconds, with a sensitivity of 94% and
3e434415a387 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/krocus commit 5d1d3bd35e5cf4bcffe3e7ad1b079eeff1162ca0-dirty
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81 specificity of 97%, directly from uncorrected raw sequence reads.
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82
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83 Documentation can be found at `<https://github.com/andrewjpage/krocus>`_.
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84 ]]>
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85 </help>
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86 <expand macro="citations" />
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87 </tool>